Explore Workflows

**VCF to GDS** workflow converts VCF or BCF files into Genomic Data Structure (GDS) format. GDS files are required by all workflows utilizing the GENESIS or SNPRelate R packages. _Filename requirements_: The input file names should follow the pattern <A>chr<X>.<y> For example: 1KG_phase3_subset_chr1.vcf.gz Some of the tools inside the workflow infer the chromosome number from the file by expecting this pattern of file name.

https://github.com/sevenbridges-openworkflows/uw-genesis-topmed-cwl.git

Path: vcftogds/vcf-to-gds-wf.cwl

Branch/Commit ID: master

https://github.com/mliukis/sounder-sips-application.git

Path: cwl/l1a_workflow.cwl

Branch/Commit ID: main

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/env-wf2.cwl

Branch/Commit ID: main

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/env-wf1.cwl

Branch/Commit ID: master

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: tools/tRNA_selection.cwl

Branch/Commit ID: 8515542

https://gitlab.ebrains.eu/sofiakar/yre-standardised-workflows.git

Path: Workflows/PSD_workflow_bucket_1/workflow.cwl

Branch/Commit ID: main

https://github.com/EOSC-LOFAR/presto-cwl.git

Path: birds.cwl

Branch/Commit ID: visualise

The main workflow that: produces two reproducible peaks via IDR given two eCLIP samples (1 input, 1 IP each). runs the 'rescue ratio' statistic runs the 'consistency ratio' statistic

https://github.com/YeoLab/merge_peaks.git

Path: cwl/wf_full_IDR_pipeline_2inputs.cwl

Branch/Commit ID: master

Workflow without inputs.

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/no-inputs-wf.cwl

Branch/Commit ID: master

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: master